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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGCAGACTGAGGCAACTATGAGCGCAGAGGTGGAGTTGATTTCTACTATGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacacttgcccccaattggaggacacacattttttttgctttattttgtctattgcaattcggaactggatatggatagtagcagagagcttaaat...

Basic information

species Zea mays
transcript GRMZM2G331032_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G331032_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g46510.1 (Oryza sativa), 5'ss of exon 11
TGGGCAGACTGAGGCAACTATGAGCGCAGAGGTGGAGTTGATTTCTACTATGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacacttgcccccaattggaggacacacattttttttgctttattt--tgtctattgcaattcggaactggatatggatagtagcagagagcttaaat
||| || ||||||||||| ||||| || || || ||| |||||||||| ||||| |||||||| ||||||||||| || || || |||||||||||||||||  ||   || || ||  ||| |  || | | | |  || ||   || |     | | | || ||      ||    |  | |  |    |      | ||
TGGACAAACTGAGGCAACCATGAGTGCCGAAGTTGAGCTGATTTCTACAATGGGGGAAAAGAAATCATGGAACAGGCCGCCAATTCAGATGGAATTCCAGgt--taattttacctccttttgaacaaccctcttatcattagcaaaatctgtcagccagttcattttatttttgagcttacagaaaatgcaatgttagagat

upper sequence: GRMZM2G331032_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv02s0012g00910.t01 (Vitis vinifera), 5'ss of exon 11
TGGGCAGACTGAGGCAACTATGAGCGCAGAGGTGGAGTTGATTTCTACTATGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgta---atacacttgcccccaattggaggacacacattttttttgctttattttgtctattgcaattcggaactggatatggatagtagcagagagcttaaat
||| || |||||| |||| ||||| ||||| || ||||||||||| || ||||  ||||||||||| |||| ||| ||||| || ||||||||||||||||||   | | |  |         |  |  | |     ||| | || |    ||| |||| |  ||| |  |    |||  || || |  ||||   |   || 
TGGACAAACTGAGCCAACAATGAGTGCAGAAGTAGAGTTGATTTCCACGATGGCAGAAAAGAAGTCTTGGACCAGGCCACCGATTCAGATGGAATTCCAGgtacctaaaaaaatatttttctgtacatcagagtggctttatatgataatgtttttctactataatgc--attctgatgaggttaatgccagaattcaggaa-
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|149083895|gb|EE173270.2|EE173270
EST:     TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAG                         GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
genomic: TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
EST: gi|60356037|gb|DN223010.1|DN223010
EST:     TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAG                         GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
genomic: TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
EST: gi|18660565|gb|BM500930.1|BM500930
EST:     GGTGAAAAGAAGTCATGGGAACAGACCAC-TATCCAGATGGGAATTCC-G                         GTTCCAATGTTCACTGCTTCTGGGTTACGTGTTNGCTTCNTTAA
genomic: GGTGAAAAGAAGTCATGG-AACAGACCACCTATCCAGATGG-AATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAA
EST: gi|5847424|gb|AW000503.1|AW000503
EST:     TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAG                         GTTCCAATGTTCNCTGCNTCTGGTTTACGTGTTCGCTTCCTTAAG
genomic: TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
EST: gi|4886096|gb|AI677216.1|AI677216
EST:     TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAG                         GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
genomic: TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
EST: gi|78022244|gb|DV490631.1|DV490631
EST:     TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAG                         GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
genomic: TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
EST: gi|60354626|gb|DN221599.1|DN221599
EST:     TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAG                         GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
genomic: TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
EST: gi|6012529|gb|AW061966.1|AW061966
EST:     CTATCCAGATGGAATTCCAG                         GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
genomic: CTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
EST: gi|7145566|gb|AW507047.1|AW507047
EST:     TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAG                         GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
genomic: TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
EST: gi|37396642|gb|CF635614.1|CF635614
EST:     GACCACCTATCCAGATGGAATTCCAG                         GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
genomic: GACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
EST: gi|76282278|gb|DV021846.1|DV021846
EST:     TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAG                         GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
genomic: TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
EST: gi|71304028|gb|DR788135.1|DR788135
EST:     TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAG                         GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
genomic: TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
EST: gi|211534676|gb|FL445694.1|FL445694
EST:     TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAG                         GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
genomic: TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
EST: gi|211271326|gb|FL168764.1|FL168764
EST:     TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAG                         GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
genomic: TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
EST: gi|6101968|gb|AW126438.1|AW126438
EST:     TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAG                         GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
genomic: TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
EST: gi|37375113|gb|CF623970.1|CF623970
EST:     TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAG                         GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
genomic: TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
EST: gi|4609486|gb|AI600325.1|AI600325
EST:     TGGGTGAAAAGAAGTCATGGAACAGACCNCCTATCCAGATGGAATTCCAG                         GTTCCAATGTTCNCTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
genomic: TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
EST: gi|91054998|gb|EB165416.1|EB165416
EST:     GGAGTTGATTTCTACTATGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCCAG        
genomic: GGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCC-AGgtaatacact ... ggtcatgtagG
EST: gi|91054997|gb|EB165415.1|EB165415
EST:     TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAG                         GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
genomic: TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
EST: gi|31250241|gb|CD219265.1|CD219265
EST:     GGGTGAAAAGAAGTCATGGAACAGACCACCTATCCNGATGGAATTCCAG                         GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
genomic: GGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
EST: gi|32932355|gb|CF037167.1|CF037167
EST:     TGGGTGAAAAGAAGCCATGGAACAGACCACCTATCCAGATGGAATTCCAG                         GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
genomic: TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
EST: gi|32932405|gb|CF037217.1|CF037217
EST:     TGGGTGAAAAGAAGCCATGGAACAGACCACCTATCCAGATGGAATTCCAG                         GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
genomic: TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
EST: gi|37383436|gb|CF628735.1|CF628735
EST:     TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAG                         GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
genomic: TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG
EST: gi|31354959|gb|CD439316.1|CD439316
EST:     TGGAGTTGATTTCTACTATGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAG        
genomic: TGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 157

TGGGCAGACTGAGGCAACTATGAGCGCAGAGGTGGAGTTGATTTCTACTATGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 222

TGGGCAGACTGAGGCAACTATGAGCGCAGAGGTGGAGTTGATTTCTACTATGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 342

TGGGCAGACTGAGGCAACTATGAGCGCAGAGGTGGAGTTGATTTCTACTATGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 165

TGGGCAGACTGAGGCAACTATGAGCGCAGAGGTGGAGTTGATTTCTACTATGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacact ... ggtcatgtagGTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGCAGACTGAGGCAACTATGAGCGCAGAGGTGGAGTTGATTTCTACTATGGGTGAAAAGAAGTCATGGAACAGACCACCTATCCAGATGGAATTCCAGgtaatacacttgcccccaattggaggacacacattttttttgctttattttgtctattgcaattcggaactggatatggatagtagcagagagcttaaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgccccc